Basic Information
VIS ID
TVIS30002120
Fusion event
HIV-KDM2B integration
Validated
No
Detection method
QiaQuick PCR and Sequencing
Data source
download(RID)
Sample type
Cell line
Disease
HIV-infected disease (HID)
Quality evaluation
Normal
Reported year
2013
PubMed ID
23953889
Virus Sequence
Virus name
HIV
Reference genome
Not given
Host Sequence
Chromosome
chr12
Cytoband
q24.31
Reference genome
GRCh37/hg19
Start
121921234/121483431 (Hg38)
End
121921234/121483431 (Hg38)
Orient
+
Location type
Intronic
Fragile sites / regions
FRA12E
Target gene
KDM2B
miRNAs that regulate target gene
hsa-mir-1-3p ; hsa-mir-324-3p ; hsa-mir-6783-3p ; hsa-mir-1343-3p ; hsa-mir-4772-3p ; hsa-mir-3605-3p ; hsa-mir-6787-3p ; hsa-mir-1304-3p ; hsa-mir-6774-3p ; hsa-mir-6742-3p ; hsa-mir-6852-5p ; hsa-mir-939-3p ; hsa-mir-6736-3p ; hsa-mir-6890-3p ; hsa-mir-216a-5p ; hsa-mir-6722-5p ; hsa-mir-652-3p ; hsa-mir-5197-5p ; hsa-mir-146a-5p ; hsa-mir-448
Nearest miRNA
hsa-let-7i/Upstream/39079; hsa-mir-3612/Downstream/1212476;
Nearest TSS
ENST00000382841/Upstream/12878; ENST00000541574/Downstream/26275;
Nearest CpG islands
None/Target, chr12-CpG: 104/Upstream/15278, chr12-CpG: 131/Downstream/53692
Upstream sequence
GCTCCGTTCACATATGTCCAGTCAACCAAAATGCAGAGTAGACCGGTATTAGGCCCTATggccaggtgcagtggctcacgcctgtaatcctagcactttg
Downstream sequence
ggaggctgaggcaggcggatctcttgagcccaggagattgagaccagccttggcagcatggcaagaccccatctctactaaaaaaaatacgaaaatttaa
Reference
Sherrill-Mix, S., et al. HIV latency and integration site placement in five cell-based models.2013, Retrovirology 10: 90.
Curate